I'm assuming you already have "Use a Global DCV Passthrough instead of .htaccess modification (requires EA4)" enabled under the "Domains" tab in "WHM >> Tweak Settings". If so, here are a couple of rules you could add to the .htaccess file that have worked for others facing the same issue:
Code:
RewriteCond %{REQUEST_URI} !^/[0-9]+\..+\.cpaneldcv$
RewriteCond %{REQUEST_URI} !^/\.well-known/pki-validation/[A-F0-9]{32}\.txt(?:\ Comodo\ DCV)?$